Cold-induced Genes Research Articles

Isolation and functional characterization of cold-regulated promoters, by digitally identifying peach fruit cold-induced genes from a large EST dataset

BackgroundCold acclimation is the process by which plants adapt to the low, non freezing temperatures that naturally occur during late autumn or early winter. This process enables the plants to resist the freezing temperatures of winter. Temperatures similar to those associated with cold acclimation are also used by the fruit industry to delay fruit ripening in peaches. However, peaches that are subjected to long periods of cold storage may develop chilling injury symptoms (woolliness and internal breakdown). In order to better understand the relationship between cold acclimation and chilling injury in peaches, we isolated and functionally characterized cold-regulated promoters from cold-inducible genes identified by digitally analyzing a large EST dataset.ResultsDigital expression analyses of EST datasets, revealed 164 cold-induced peach genes, several of which show similarities to genes associated with cold acclimation and cold stress responses. The promoters of three of these cold-inducible genes (Ppbec1, Ppxero2 and Pptha1) were fused to the GUS reporter gene and characterized for cold-inducibility using both transient transformation assays in peach fruits (in fruta) and stable transformation in Arabidopsis thaliana. These assays demonstrate that the promoter Pptha1 is not cold-inducible, whereas the Ppbec1 and Ppxero2 promoter constructs are cold-inducible.ConclusionThis work demonstrates that during cold storage, peach fruits differentially express genes that are associated with cold acclimation. Functional characterization of these promoters in transient transformation assays in fruta as well as stable transformation in Arabidopsis, demonstrate that the isolated Ppbec1 and Ppxero2 promoters are cold-inducible promoters, whereas the isolated Pptha1 promoter is not cold-inducible. Additionally, the cold-inducible activity of the Ppbec1 and Ppxero2 promoters suggest that there is a conserved heterologous cold-inducible regulation of these promoters in peach and Arabidopsis. These results reveal that digital expression analyses may be used in non-model species to identify candidate genes whose promoters are differentially expressed in response to exogenous stimuli.

In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control

Motivation:Cold acclimation involves a number of different cellular processes that together increase the freezing tolerance of an organism. The DREB1/CBFs are transcription factors (TFs) that are prominent in the regulation of cold responses in Arabidopsis thaliana, rice and many other crops. We investigated if the expression of DREB1/CBFs and co-expressed genes relies on combinatorial control by several TFs. Our results support this notion and indicate that methods for studying the regulation of complex cellular processes should include identification of combinations of motifs, in addition to searching for individual overrepresented binding sites.Contact:angelica.lindlof@his.seSupplementary information:Supplementary data are available at Bioinformatics online.

Roles forArabidopsisCAMTA Transcription Factors in Cold-Regulated Gene Expression and Freezing Tolerance

The Arabidopsis thaliana CBF cold response pathway plays a central role in cold acclimation. It is characterized by rapid cold induction of genes encoding the CBF1-3 transcription factors, followed by expression of the CBF gene regulon, which imparts freezing tolerance. Our goal was to further the understanding of the cis-acting elements and trans-acting factors involved in expression of CBF2. We identified seven conserved DNA motifs (CM), CM1 to 7, that are present in the promoters of CBF2 and another rapidly cold-induced gene encoding a transcription factor, ZAT12. The results presented indicate that in the CBF2 promoter, CM4 and CM6 have negative regulatory activity and that CM2 has both negative and positive activity. A Myc binding site in the CBF2 promoter was also found to have positive regulatory effects. Moreover, our results indicate that members of the calmodulin binding transcription activator (CAMTA) family of transcription factors bind to the CM2 motif, that CAMTA3 is a positive regulator of CBF2 expression, and that double camta1 camta3 mutant plants are impaired in freezing tolerance. These results establish a role for CAMTA proteins in cold acclimation and provide a possible point of integrating low-temperature calcium and calmodulin signaling with cold-regulated gene expression.

The Novel Approach Towards Estimation of Frost Tolerance in Barley

ABSTRACTWe developed a convenient, efficient and reliable PCR-based technique to distinguish the frost tolerant and sensitive genotypes in barley. Based on artificial freeze test, significant differences among genotypes were found. In these plants, frost tolerance, expressed as LT50, was strongly correlated with the existence of cold-induced genes. Comparison of LT50 values and the PCR-detected pattern of cold-induced genes showed that Hudson, Dictoo and Krusevac occupied three first positions in terms of a high frost tolerance. After 35 and 49 days of cold acclimation, the Nortstar was found to be the most tolerant wheat genotype (LT50: -16°C). Low correlation between LT50 and existence of cold-induced genes was found for rye and wheat genotypes. Diploid forms of rye plants were found to be more frost tolerant than tetraploid forms.

Over-expression of a cold-induced plasma membrane protein gene ( MpRCI) from plantain enhances low temperature-resistance in transgenic tobacco

The plasma membrane is the most direct target of low temperature injury in plants. We have cloned a cold-induced gene ( MpRCI) from plantain ( Musa paradisiaca L.; ABB Group). Expression of an MpRCI::GFP fusion protein in onion epidermal cells showed localization of the protein product in the plasma membrane. The expression profile of MpRCI was analyzed by RT-PCR and the results indicated that MpRCI is induced by low temperatures in leaves and leafstalk, but not in the shoot meristematic or roots. We also cloned a 1.2 kb fragment upstream of MpRCI, predicted to contain several elements related to abiotic stresses, and demonstrated that the sequence has characteristics of low temperature- and ABA-induced promoter activity. Furthermore, the results of the phenotypic espial and ion leakage assays, using transgenic tobacco containing the gene, indicated that over-expression of the cold-induced plasma membrane protein gene MpRCI enhanced low temperature-resistance in the these plants. These results suggest that MpRCI is involved in maintaining the stability of the plasma membrane at low temperatures.

Low temperature stress in maize (Zea mays L.) induces genes involved in photosynthesis and signal transduction as studied by suppression subtractive hybridization

Unfavourable environmental conditions such as cold induce the transcription of a range of genes in plants in order to acclimate to these growth conditions. To better understand the cold acclimation of maize (Zea mays L.) it is important to identify components of the cold stress response. For this purpose, cold-induced genes were analysed using the PCR-select cDNA subtraction method. We identified several novel genes isolated from maize seedling exposed for 48h to 6 degrees C. Of 18 Zea mays cold-induced genes (ZmCOI genes) characterized, the majority share similarities with proteins with known function in signal transduction and photosynthesis regulation. RT-PCR was conducted for a selected group of genes, namely ZmCOI6.1, ZmACA1, ZmDREB2A and ZmERF3, confirming the induction by low temperature. In addition, it was found that their expression was strongly induced by other abiotic stresses such as drought and high salt concentration, by stress signalling molecules such as jasmonic acid, salicylic acid and abscisic acid, and by membrane rigidification. These results suggest that this group of genes is involved in a general response to abiotic stresses.

Role of cytokinin and salicylic acid in plant growth at low temperatures

Low temperature restrains plant growth by inhibiting the cell cycle, and phytohormones play important roles in this case; however, the molecular mechanisms whereby phytohormones affect growth at low temperature are largely unknown. When grown at 23, 16, 10, and 4°C, we found that Arabidopsis thaliana could develop with normal morphology, but needed a prolonged period of cultivation. By screening mutants, we could implicate cytokinin and salicylic acid. At 4°C, both amp1 plants, which have an increased level of cytokinin, and wild-type plants treated with exogenous cytokinin, displayed relative growth rates greater than control by increasing total cell number. Additionally, transgenic NahG plants, which have lower salicylic acid content, grew faster than wild-type accompanied by larger cells. Expression of C-repeat binding transcription factors (CBFs), that mediate cold acclimation by stimulation of the expression of cold-inducible genes, was similar in all tested genotypes. Thus CBF expression did not correlate with the observed enhanced growth in mutants. The improved growth coincided with elevated expression of CYCD3;1, especially in NahG plants. At 4°C, enhanced endoreduplication took responsibility for larger cells in NahG plants, while enhanced cell division was observed in amp1 plants.

Osmyb4 expression improves adaptive responses to drought and cold stress in transgenic apples

Constitutive expression of the rice cold-inducible Osmyb4 gene in transgenic Arabidopsis (Arabidopsis thaliana) plants improves adaptive responses to cold and drought stress, most likely due to the constitutive activation of several stress-inducible pathways and to the accumulation of several compatible solutes (e.g., glucose, fructose, sucrose, proline, glycine betaine and some aromatic compounds). Although the Osmyb4 gene seems able to activate stress responsive pathways in different species, we previously reported that its specific effect on stress tolerance depends on the transformed species. In the present work, we report the effects of the Osmyb4 expression for improving the stress response in apple (Malus pumila Mill.) plants. Namely, we found that the ectopic expression of the Myb4 transcription factor improved physiological and biochemical adaptation to cold and drought stress and modified metabolite accumulation. Based on these results it may be of interest to use Osmyb4 as a tool for improving the productivity of woody perennials under environmental stress conditions.

Development of ChillPeach genomic tools and identification of cold-responsive genes in peach fruit

The ChillPeach database was developed to facilitate identification of genes controlling chilling injury (CI), a global-scale post-harvest physiological disorder in peach. It contained 7,862 high-quality ESTs (comprising 4,468 unigenes) obtained from mesocarp tissues of two full-sib progeny contrasting for CI, about 48 and 13% of which are unique to Prunus and Arabidopsis, respectively. All ESTs are in the Gateway vector to facilitate functional assessment of the genes. The data set contained several putative SNPs and 184 unigenes with high quality SSRs, of which 42% were novel to Prunus. Microarray slides containing 4,261 ChillPeach unigenes were printed and used in a pilot experiment to identify differentially expressed genes in cold-treated compared to control mesocarp tissues, and in vegetative compared to mesocarp tissues. Quantitative RT-PCR (qRT-PCR) confirmed microarray results for all 13 genes tested. The microarray and qRT-PCR analyses indicated that ChillPeach is rich in putative fruit-specific and novel cold-induced genes. A website ( http://bioinfo.ibmcp.upv.es/genomics/ChillPeachDB ) was created holding detailed information on the ChillPeach database.

Expression of dehydrin 5 during the development of frost tolerance in barley ( Hordeum vulgare)

The Dhn5 gene is the major cold-inducible dehydrin gene in barley. This study deals with the relationship between Dhn5 gene expression and its protein product accumulation, and the development of frost tolerance (FT) upon cold acclimation (CA) in 10 barley cultivars of different growth habits and geographical origins. The activation of Dhn5 gene expression was determined by quantitative reverse transcription-polymerase chain reaction (qRT-PCR), the accumulation of DHN5 protein was evaluated by protein gel blot analysis using a specific anti-dehydrin antibody, and the acquired level of FT was determined by a direct frost test. During the first 2 weeks of CA, there was a rapid increase in Dhn5 gene expression, DHN5 protein accumulation and FT in all cultivars examined. After 2 weeks of CA, differences in DHN5 accumulation and in FT measured as lethal temperature (LT(50)) were observed between the cultivars belonging to different growth habits. Specifically, intermediate (I) and winter (W) cultivars showed a higher level of DHN5 accumulation and FT than the spring (S) cultivars, which exhibited a lower level of accumulated DHN5 and FT. (Intermediate cultivars do not have vernalization requirement, but they are able to induce a relatively high level of FT upon CA.) In contrast, no differences between the cultivars belonging to different growth habits in Dhn5 mRNA accumulation were found. After 3 weeks of CA, the differences in accumulated DHN5 and FT between the individual growth habits became evident due to different developmental regulation of FT. The amount of accumulated DHN5 corresponded well with the level of FT of individual cultivars. We conclude that the amount of accumulated DHN5 after a certain period of CA differed according to the growth habits of cultivars and can be used as a marker for determination of FT in barley.

Regulatory mechanisms involved in cold acclimation response: a review

Freezing temperatures are one of the environmental stresses with more impact in plant development in temperate regions. By means of cold acclimation, many plant species are able to increase their freezing tolerance in response to low-nonfreezing temperatures. In the last years, an important effort has been made to characterize the molecular mechanisms that control this adaptive process. Transcriptome analyses indicate that cold acclimation is mainly regulated by low temperatures through changes in gene expression. In this regard, it has been reported that 3.4% of Arabidopsis genes are regulated by low temperature, including 95 genes annotated as transcription factors. The control of coldinducible gene expression is very complex and involves many different signaling pathways that, in some cases, seem to share common intermediates. Interestingly, recent reports have shown that RNA processing and export, as well as post-translational modifications, including ubiquitylation and SUMOylation, also play important roles in regulating cold acclimation. Furthermore, histone modifications seem to be relevant in this regulation. In fact, histone acetylation and deacetylation are needed for correct activation of gene expression in response to low temperatures. All these data reveal that post-transcriptional mechanisms should be taken into consideration when analyzing the control of cold acclimation. Following, is a brief overview of the current understanding on the regulatory mechanisms that ensures the accurate development of this adaptive response.

Posttranscriptional regulation ofcspEinEscherichia coli: involvement of the short 5′-untranslated region

Escherichia coli K-12 contains nine paralogs of CspA, namely CspA-CspI. In spite of considerable sequence similarity among these genes, the individual members of this family show significant differences in their expression regulation. Among these nine members, cspA, B, G and I have been reported to be cold-induced. The unusually long 5'-untranslated region (5'-UTR) of these four and other cold-induced genes has often been associated with their inducibility. Sequence analysis of the cspE upstream region revealed two promoter-like motifs having high scores. We identified the promoter site and established that cspE has a much shorter 5'-UTR compared to other cold-induced genes. Our results showed that cspE is induced to about threefold at both the transcript and the protein level in response to cold-shock. Its transcript half-life increases significantly upon cold-shock. Furthermore, we demonstrated that RNase E, a key endonuclease responsible for mRNA degradation in E. coli, regulates cspE transcript stability, possibly through the assembly of a degradosome. In silico analysis of the cspE 5'-UTR revealed alternative secondary structures at 37 and 15 degrees C. A point mutation that was predicted to relax the secondary structure of the 5'-UTR at 15 degrees C showed considerable reduction in transcript stability, indicating that alternative transcript secondary structures might be the cause of the differential stability.

Molecular cloning and characterization of cold-responsive gene Cbrci35 from Capsella bursa-pastoris

A new rare cold-inducible (RCI) gene designated Cbrci35 was cloned from Capsella bursa-pastoris, an edible wild herb, using the rapid amplification of cDNA ends (RACE) method. The full-length cDNA of Cbrci35 (Database Accession No.: AY566573) was 1300 bp and contained a 978 bp ORF encoding a precursor of 326 amino acid residues with a 23 amino acids signal peptide. The predicted Cbrci35 protein contained a peroxidase active site and proximal heme-ligand signatures, an RGD cell attachment sequence motif and two leucine zipper pattern motifs. Bioinformatics analysis revealed that Cbrci35 has a high level of similarity with RCI genes from Arabidopsis thaliana and peroxidases genes from other plants. RT-PCR analysis revealed that Cbrci35 expressed only in root. A cold acclimation assay showed that Cbrci35 was expressed immediately after cold triggering, but this expression was transient, suggesting that it concerns cold acclimation. But expression was not induced exposed to dehydration, salt stress or abscisic acid, indicating that it might be subjected specifically to cold regulation. These results indicate that Cbrci35 is an analogue of RCI genes and may participate in cold-response or increasing the freezing tolerance of plants.

Isolation and Characterization of a Cold-Induced DREB Gene from Aloe Vera L.

A new cold-induced dehydration-responsive element-binding (DREB) gene encoding an AP2/ethylene response element binding protein transcription factor was isolated from Aloe vera L. by rapid amplification of complementary DNA ends (RACE). The deduced protein contained a putative acidic activation domain and an AP2 DNA binding domain of 64 amino acids. The expression analysis showed that the transcripts accumulated rapidly under cold stress and peaked at 12 h, then decreased to the original level. Yeast one-hybrid analysis indicated that Aloe DREB1 can bind to DRE cis-elements and activate the expressions of reporter genes, but the binding and activation abilities were weak. Aloe DREB1 localized in nucleus, although it lacks typical nuclear localization signal. These results implied that Aloe DREB1 might function as a transcription activator involved in the regulation of cold-responsive genes via signal transduction pathway dependent or independent of the DREB transcription factor.

Gene expression associated with increased supercooling capability in xylem parenchyma cells of larch (Larix kaempferi)

Xylem parenchyma cells (XPCs) in larch adapt to subfreezing temperatures by deep supercooling, while cortical parenchyma cells (CPCs) undergo extracellular freezing. The temperature limits of supercooling in XPCs changed seasonally from -30 degrees C during summer to -60 degrees C during winter as measured by freezing resistance. Artificial deacclimation of larch twigs collected in winter reduced the supercooling capability from -60 degrees C to -30 degrees C. As an approach to clarify the mechanisms underlying the change in supercooling capability of larch XPCs, genes expressed in association with increased supercooling capability were examined. By differential screening and differential display analysis, 30 genes were found to be expressed in association with increased supercooling capability in XPCs. These 30 genes were categorized into several groups according to their functions: signal transduction factors, metabolic enzymes, late embryogenesis abundant proteins, heat shock proteins, protein synthesis and chromatin constructed proteins, defence response proteins, membrane transporters, metal-binding proteins, and functionally unknown proteins. All of these genes were expressed most abundantly during winter, and their expression was reduced or disappeared during summer. The expression of all of the genes was significantly reduced or disappeared with deacclimation of winter twigs. Interestingly, all but one of the genes were expressed more abundantly in the xylem than in the cortex. Eleven of the 30 genes were thought to be novel cold-induced genes. The results suggest that change in the supercooling capability of XPCs is associated with expression of genes, including genes whose functions have not been identified, and also indicate that gene products that have been thought to play a role in dehydration tolerance by extracellular freezing also have a function by deep supercooling.

The Anesthetic Management of Children with Neonatal-Onset Multi-System Inflammatory Disease

Neonatal-onset multi-system inflammatory disease (NOMID), a rare autosomal dominantly inherited disease, belongs to a growing spectrum of autoinflammatory diseases, is characterized by urticarial rash, arthropathy, and chronic aseptic meningitis, and is associated with mutations in the cold-induced autoinflammatory gene, CIAS1, the gene that encodes the protein, cryopyrin. As little is known about the anesthetic considerations of the disease, we sought to identify the main features and respective anesthetic and perioperative implications of NOMID. We examined perianesthetic records of children with NOMID who were anesthetized for invasive diagnostic and therapeutic interventions between 2003 and 2006. In addition, we conducted an extensive literature review of the genetic, clinical, and biochemical abnormalities of the disease. Seventeen children with NOMID (median age 8 yr, range 9 mo to 11 yr) were anesthetized for diagnostic and therapeutic procedures. All patients had neurological involvement, including increased intracranial pressure, chronic aseptic meningitis, and developmental delay; 7 had bony overgrowth, 15 ocular, and 14 otological manifestations of NOMID. Despite the complexity of the disease, the perioperative course was uncomplicated, and no serious adverse events were observed. This study is the first to investigate the anesthetic implications of NOMID, an autoinflammatory disease associated with arthropathy, recurrent fevers, urticarial rash, and chronic aseptic meningitis. While for the pediatric anesthesiologist, the presence of fever and aseptic meningitis might make the conduct of anesthetics for elective procedures less desirable, our findings suggest that without evidence of active infection, even in the presence of fever and chronic aseptic meningitis, general and regional anesthesia may be conducted in patients with NOMID without untoward complications.

Expression levels of barley Cbf genes at the Frost resistance‐H2 locus are dependent upon alleles at Fr‐H1 and Fr‐H2

Genetic analyses have identified two loci in wheat and barley that mediate the capacity to overwinter in temperate climates. One locus co-segregates with VRN-1, which affects the vernalization requirement. This locus is known as Frost resistance-1 (Fr-1). The second locus, Fr-2, is coincident with a cluster of more than 12 Cbf genes. Cbf homologs in Arabidopsis thaliana play a key regulatory role in cold acclimatization and the acquisition of freezing tolerance. Here we report that the Hordeum vulgare (barley) locus VRN-H1/Fr-H1 affects expression of multiple barley Cbf genes at Fr-H2. RNA blot analyses, conducted on a 'Nure'x'Tremois' barley mapping population segregating for VRN-H1/Fr-H1 and Fr-H2, revealed that transcript levels of all cold-induced Cbf genes at Fr-H2 were significantly higher in recombinants harboring the vrn-H1 winter allele than in recombinants harboring the Vrn-H1 spring allele. Steady-state Cbf2 and Cbf4 levels were also significantly higher in recombinants harboring the Nure allele at Fr-H2. Additional experiments indicated that, in vrn-H1 genotypes requiring vernalization, Cbf expression levels were dampened after plants were vernalized, and dampened Cbf expression was accompanied by robust expression of Vrn-1. Cbf levels were also significantly higher in plants grown under short days than under long days. Experiments in wheat and rye indicated that similar regulatory mechanisms occurred in these plants. These results suggest that VRN-H1/Fr-H1 acts in part to repress or attenuate expression of the Cbf at Fr-H2; and that the greater level of low temperature tolerance attributable to the Nure Fr-H2 allele may be due to the greater accumulation of Cbf2 and Cbf4 transcripts during normal growth and development.

Complementation Analysis of the Cold-Sensitive Phenotype of the Escherichia coli csdA Deletion Strain

The cold shock response of Escherichia coli is elicited by downshift of temperature from 37 degrees C to 15 degrees C and is characterized by induction of several cold shock proteins, including CsdA, during the acclimation phase. CsdA, a DEAD-box protein, has been proposed to participate in a variety of processes, such as ribosome biogenesis, mRNA decay, translation initiation, and gene regulation. It is not clear which of the functions of CsdA play a role in its essential cold shock function or whether all do, and so far no protein has been shown to complement its function in vivo. Our screening of an E. coli genomic library for an in vivo counterpart of CsdA that can compensate for its absence at low temperature revealed only one protein, RhlE, another DEAD-box RNA helicase. We also observed that although not detected in our genetic screening, two cold shock-inducible proteins, namely, CspA, an RNA chaperone, and RNase R, an exonuclease, can also complement the cold shock function of CsdA. Interestingly, the absence of CsdA and RNase R leads to increased sensitivity of the cells to even moderate temperature downshifts. The correlation between the helicase activity of CsdA and the stability of mRNAs of cold-inducible genes was shown using cspA mRNA, which was significantly stabilized in the DeltacsdA cells, an effect counteracted by overexpression of wild-type CsdA or RNase R but not by that of the helicase-deficient mutant of CsdA. These results suggest that the primary role of CsdA in cold acclimation of cells is in mRNA decay and that its helicase activity is pivotal for promoting degradation of mRNAs stabilized at low temperature.

Overexpression of OsCOIN, a putative cold inducible zinc finger protein, increased tolerance to chilling, salt and drought, and enhanced proline level in rice

Rice (Oryza sativa L.) plant is sensitive to chilling, particularly at early stages of seedling development. Here a novel cold-inducible gene, designated OsCOIN (Oryza sativa cold-inducible), was isolated and characterized. Results showed that OsCOIN protein, a RING finger protein, was localized in both nuclear and cytoplasm membrane. OsCOIN is expressed in all rice organs and strongly induced by low temperature, ABA, salt and drought. Over-expression of OsCOIN in transgenic rice lines significantly enhanced their tolerance to cold, salt and drought, accompanied by an up-regulation of OsP5CS expression and an increase of cellular proline level.

Nonclassic Neurologic Features in Cryopyrin-Associated Periodic Syndromes

Neurologic manifestations in early childhood occur in the cryopyrin-associated periodic syndromes, especially in the chronic infantile neurological, cutaneous, and articular syndrome (CINCA) and the Muckle-Wells syndrome. Cryopyrin-associated periodic syndromes are commonly linked to mutations in the cold-induced autoinflammatory syndrome gene CIAS1 (current symbol, NLRP3) on chromosome 1. We describe three children with atypical cryopyrin-associated periodic syndromes, neurologic symptoms, and a Q705K mutation. Cryopyrin-associated periodic syndrome screening should be considered for children with neurologic and other periodic symptoms with elevated inflammatory markers. This syndrome is treatable with anakinra.